I figured I'd stop by and give an aftermath of the happenings.
Things work now --- but I am very confused why and how --- I suspect I will never actually get the answer.
As I had mentioned, I ended up setting up an Ubuntu Workstation and configured it mostly as a server installing several different network services from a guide I had found that focused on setting Ubuntu up like a router.
That didn't ultimately work, so I tried creating a bridge between the two connections instead of setting up a connection sharing.
That didn't work and that's about where I stopped for a while. I decided to hammer down legal options for a while because, truthfully, I was dragging my feat on the prospects of reinstalling the original firmware to use the fork.
Thats where everything sat for about 2 weeks or so.
With the legal options being long and complicated, I decided to give a few more things a try. Low and behold, things MAGICALLY started working.
I don't know if Ubuntu grabbed a patch that resolved things, if my apartment complex changed something or updated something on their side or what, but through no additional troubleshooting on my side things were now resolved. I'd be inclined to think it was more of the later then the former, but the former could be possible too.
As it stands right now, I have my connection running from the jack into the Ubuntu Server then into the RT-N66U with the latest version of Merlin for many of the connections with it in Router Mode and the connection plugged into the WAN port.
I'm mystified what actually fixed it, but I'm glad its done.
Thanks very much for help in resolving the issue.